Chung Tsai wrote:

I was wondering if there is a way to calculate the voltage drop between sites i and j (Vj-Vi) for any given pair of sites in the system?

You can attach leads as "voltage probes" to the sites of interest and then use https://kwant-project.org/doc/1/reference/generated/kwant.solvers.common.SMa....

However this will be an approximation, since Kwant does not solve the Poisson equation.